added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index aa47940a030f968e02686b915d26e84c29584b8d..bc1cdb3ecfaa8ca528b88c2534e40c61263aacef 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -56,7 +56,30 @@ string SplitAbundCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string SplitAbundCommand::getOutputFileNameTag(string type, string inputName=""){      
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta")            {   outputFileName =  "fasta";   }
+            else if (type == "list")    {   outputFileName =  "list";   }
+            else if (type == "name")        {   outputFileName =  "names";   }
+            else if (type == "group")       {   outputFileName =  "groups";   }
+            else if (type == "accnos")        {   outputFileName =  "accnos";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitAbundCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 SplitAbundCommand::SplitAbundCommand(){        
        try {
@@ -181,7 +204,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);         
                        if (groups == "not found") { groups = ""; }
                        else if (groups == "all") { 
-                               if (groupfile != "") {  Groups = groupMap->namesOfGroups;  } 
+                               if (groupfile != "") {  Groups = groupMap->getNamesOfGroups();  } 
                                else {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";   }
                        }else { 
                                m->splitAtDash(groups, Groups);
@@ -213,10 +236,9 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        accnos = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
 
                        if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
-
                }
 
        }
@@ -250,11 +272,11 @@ int SplitAbundCommand::execute(){
                        if (namefile != "") {  readNamesFile();         }
                        else                            { createNameMap(list);  }
                        
-                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } return 0; }
                        
                        while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
+                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } return 0; }
                                
                                if(allLines == 1 || labels.count(list->getLabel()) == 1){
                                                
@@ -288,7 +310,7 @@ int SplitAbundCommand::execute(){
                                list = input->getListVector(); //get new list vector to process
                        }
                        
-                       if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -304,7 +326,7 @@ int SplitAbundCommand::execute(){
 
                        }
                        
-                       if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
                        
                        //run last label if you need to
                        if (needToRun == true)  {
@@ -319,7 +341,7 @@ int SplitAbundCommand::execute(){
                        
                        delete input;
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); }       return 0;       }
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }      return 0;       }
                                                                        
                }else { //you are using the namefile to determine abundance
                        if (outputDir == "") { outputDir = m->hasPath(namefile); }
@@ -435,11 +457,11 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag) {
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare.list";
+                       string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare." + getOutputFileNameTag("list");
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["list"].push_back(rare);
                        
-                       string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund.list";
+                       string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund." + getOutputFileNameTag("list");
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["list"].push_back(abund);
 
@@ -477,10 +499,12 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag) {
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFile(fileroot + Groups[i] + tag + ".rare.list", *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFile(fileroot + Groups[i] + tag + ".abund.list", *(filehandles[Groups[i]+".abund"]));
-                               outputNames.push_back(fileroot + Groups[i] + tag + ".rare.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".rare.list");
-                               outputNames.push_back(fileroot + Groups[i] + tag + ".abund.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".abund.list");
+                string rareGroupFileName = fileroot + Groups[i] + tag + ".rare." + getOutputFileNameTag("list");
+                string abundGroupFileName = fileroot + Groups[i] + tag + ".abund." + getOutputFileNameTag("list");
+                               m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
+                               m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
+                               outputNames.push_back(rareGroupFileName); outputTypes["list"].push_back(rareGroupFileName);
+                               outputNames.push_back(abundGroupFileName); outputTypes["list"].push_back(abundGroupFileName);
                        }
                        
                        map<string, string> groupVector;
@@ -643,11 +667,11 @@ int SplitAbundCommand::writeNames() { //namefile
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(namefile))  + "rare.names";
+                       string rare = outputDir + m->getRootName(m->getSimpleName(namefile))  + "rare." + getOutputFileNameTag("name");
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["name"].push_back(rare);
                        
-                       string abund = outputDir + m->getRootName(m->getSimpleName(namefile))  + "abund.names";
+                       string abund = outputDir + m->getRootName(m->getSimpleName(namefile))  + "abund." + getOutputFileNameTag("name");
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["name"].push_back(abund);
                        
@@ -678,8 +702,10 @@ int SplitAbundCommand::writeNames() { //namefile
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFile(fileroot + Groups[i] + ".rare.names", *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFile(fileroot + Groups[i] + ".abund.names", *(filehandles[Groups[i]+".abund"]));
+                string rareGroupFileName = fileroot + Groups[i] + ".rare." + getOutputFileNameTag("name");
+                string abundGroupFileName = fileroot + Groups[i] + ".abund." + getOutputFileNameTag("name");
+                               m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
+                               m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
                        }
                        
                        for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {                               
@@ -715,7 +741,7 @@ int SplitAbundCommand::writeNames() { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + it3->first + ".names");  outputTypes["name"].push_back(fileroot + it3->first + ".names");
+                               outputNames.push_back(fileroot + it3->first + "." + getOutputFileNameTag("name"));  outputTypes["name"].push_back(fileroot + it3->first + "." + getOutputFileNameTag("name"));
                                delete it3->second;
                        }
                }
@@ -740,7 +766,7 @@ int SplitAbundCommand::writeAccnos(string tag) {
                        ofstream rout;
                        
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(inputFile))  + tag + "rare.accnos";
+                       string rare = outputDir + m->getRootName(m->getSimpleName(inputFile))  + tag + "rare." + getOutputFileNameTag("accnos");
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["accnos"].push_back(rare); 
                        
@@ -749,7 +775,7 @@ int SplitAbundCommand::writeAccnos(string tag) {
                        }
                        rout.close();
                
-                       string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag  + "abund.accnos";
+                       string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag  + "abund." + getOutputFileNameTag("accnos");
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
                        
@@ -771,8 +797,8 @@ int SplitAbundCommand::writeAccnos(string tag) {
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare.accnos", *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund.accnos", *(filehandles[Groups[i]+".abund"]));
+                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".rare"]));
+                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".abund"]));
                        }
                        
                        //write rare
@@ -796,7 +822,7 @@ int SplitAbundCommand::writeAccnos(string tag) {
                        //close files
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + ".accnos");  outputTypes["accnos"].push_back(fileroot + tag + it3->first + ".accnos");
+                               outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos"));  outputTypes["accnos"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos"));
                                delete it3->second;
                        }
                }
@@ -819,11 +845,12 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "rare.groups";
+                       string rare = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "rare." + getOutputFileNameTag("group");
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["group"].push_back(rare);
                
-                       string abund = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "abund.groups";
+                       string abund = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "abund." + getOutputFileNameTag("group");
+;
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["group"].push_back(abund);
                        
@@ -863,8 +890,8 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare.groups", *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund.groups", *(filehandles[Groups[i]+".abund"]));
+                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".rare"]));
+                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".abund"]));
                        }
                        
                        for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {                               
@@ -890,7 +917,7 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + ".groups");  outputTypes["group"].push_back(fileroot + tag + it3->first + ".groups");
+                               outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group"));  outputTypes["group"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group"));
                                delete it3->second;
                        }
                }
@@ -913,11 +940,11 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "rare.fasta";
+                       string rare = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "rare." + getOutputFileNameTag("fasta");
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
                
-                       string abund = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "abund.fasta";
+                       string abund = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "abund." + getOutputFileNameTag("fasta");
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
                
@@ -964,8 +991,8 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare.fasta", *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund.fasta", *(filehandles[Groups[i]+".abund"]));
+                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".rare"]));
+                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".abund"]));
                        }
                        
                        //open input file
@@ -1010,7 +1037,7 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + ".fasta");  outputTypes["fasta"].push_back(fileroot + tag + it3->first + ".fasta");
+                               outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta"));  outputTypes["fasta"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta"));
                                delete it3->second;
                        }
                }